title: Genome-wide transcriptional analysis of super-embryogenic Medicago truncatula explant cultures.
abstract: BACKGROUND
  The Medicago truncatula (M. truncatula) line 2HA has a 500-fold greater capacity to regenerate plants in culture by somatic embryogenesis than its wild type progenitor Jemalong. To understand the molecular basis for the regeneration capacity of this super-embryogenic line 2HA, using Affymetrix GeneChip(R), we have compared transcriptomes of explant leaf cultures of these two lines that were grown on media containing the auxin NAA (1-naphthaleneacetic acid) and the cytokinin BAP (6-benzylaminopurine) for two weeks, an early time point for tissue culture proliferation.
  
  
  RESULTS
  Using Affymetrix GeneChip, GCRMA normalisation and statistical analysis, we have shown that more than 196 and 49 probe sets were significantly (p < 0.05) up- or down-regulated respectively more than 2 fold in expression. We have utilised GeneBins, a database for classifying gene expression data to distinguish differentially displayed pathways among these two cultures which showed changes in number of biochemical pathways including carbon and flavonoid biosynthesis, phytohormone biosynthesis and signalling. The up-regulated genes in the embryogenic 2HA culture included nodulins, transporters, regulatory genes, embryogenesis related arabinogalactans and genes involved in redox homeostasis, the transition from vegetative growth to reproductive growth and cytokinin signalling. Down-regulated genes included protease inhibitors, wound-induced proteins, and genes involved in biosynthesis and signalling of phytohormones auxin, gibberellin and ethylene. These changes indicate essential differences between the super-embryogenic line 2HA and Jemalong not only in many aspects of biochemical pathways but also in their response to auxin and cytokinin. To validate the GeneChip results, we used quantitative real-time RT-PCR to examine the expression of the genes up-regulated in 2HA such as transposase, RNA-directed DNA polymerase, glycoside hydrolase, RESPONSE REGULATOR 10, AGAMOUS-LIKE 20, flower promoting factor 1, nodulin 3, fasciclin and lipoxygenase, and a down-regulated gene ETHYLENE INSENSITIVE 3, all of which positively correlated with the microarray data.
  
  
  CONCLUSIONS
  We have described the differences in transcriptomes between the M. truncatula super-embryogenic line 2HA and its non-embryogenic progenitor Jemalong at an early time point. This data will facilitate the mapping of regulatory and metabolic networks involved in the gaining totipotency and regeneration capacity in M. truncatula and provides candidate genes for functional analysis.
authors.affiliation: Australian Research Council Centre of Excellence for Integrative Legume Research, Genomic Interactions Group, Research School of Biological Sciences, Australian National University, Canberra City, ACT 2601, Australia. nijat.imin@anu.edu.au
authors.forename: Nijat
authors.initials: N
authors.lastname: Imin
authors.forename: Nicolas
authors.initials: N
authors.lastname: Goffard
authors.forename: Mahira
authors.initials: M
authors.lastname: Nizamidin
authors.forename: Barry G
authors.initials: BG
authors.lastname: Rolfe
mesh_terms: D015342:DNA Probes / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D046913:Medicago truncatula / Q000196:embryology* / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D010937:Plant Growth Regulators / Q000096:biosynthesis; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D040901:Proteomics; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000196:embryology* / Q000235:genetics*; D015398:Signal Transduction; D046509:Tissue Culture Techniques; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D015342:DNA Probes; D010937:Plant Growth Regulators; D014157:Transcription Factors